Actually, it's probably the best faster-than-light system in science fiction. It's not how bad an idea it is that is the problem, because it's a pretty good idea.

No, the problem with stutterwarp is that you can't have ship to ship combat with vessels that move faster than light. I mean, they can avoid laser beams. They're not only moving faster than light; they're moving faster than reality. All sorts of odd things would happen. Perhaps it should be called the Schrödinger Drive, because you don't know if it will be there when your weapon payload arrives there. It might be there and not be there. This makes my head hurt.

If this is the case and we want to keep stutterwarp (I do without it in my campaign and use a different system) then we're going to have to have a good, hard look at the ramifications of the drive and extrapolate ship combat from there.

A nuclear explosion expands at the speed of light, so even a slow tug will effortlessly outrun a serious nuke detonating just in front of it. So you either soak the possible avenues that the ship can take in nukes (impossible) or laser beams (even more impossible) or you slow the ship down somehow.

A handwavium effect might be that stutterwarps interfere with each other; dropping the ship below the speed of light making them have to interact with each other. The problem that we get now is that ships are for all purposes tactically immobile. Tantalum is rare, rare enough to waste some uranium to cripple your enemy's ability to move in space. If you nuke the bugger no one can complain of the fallout or explosion unless they're next to it. This brings us to our next problem.

Space is cold. In fact, it's −273.15°c (−459.67°F in steam-engine terms).
This means that no matter what your ship is, unless you're wearing a very fluffy jumper your ship is going to be warmer than the background. If you have a nuke powerplant, it's going to be a lot warmer.
The only way to get rid of that heat is to radiate it, so no matter what you're now a brilliant orange dot on the enemy thermal sensor; a cheap and easy sensor to buy that can cover the entire surrounding of the enemy ship. Because space is almost a perfect vacuum you can't shed or internalise that heat; you either radiate or boil.

So, if you go sub-light you can't really move and you can't hide. Those Kafer ships with the impregnable armour are starting to look good.

If your enemy flings a missile at you it is hot too, and as everything is appallingly slow you have all the time in the world to focus a laser on it and make it a lot hotter. Missiles get destroyed faster than they can close with the target, because the closer it gets the better your laser focus.
So you have to play a laser beam on your enemy. Well, it's the fastest weapon so at least it will get there, but will it do any damage?

You have to superheat the hull so that it cannot conduct the heat away, at that point the structure will give way (burn or melt) and you can let the vacuum in, the air out and more laser in. However, over that distance you'll be having an almost impossible time getting enough focus to heat up something the size of a coin on the hull, and all the enemy has to do is move (which means you only heat up a line) or rotate their hull (so you heat up a squiggly line) to foil your efforts. At 100,000km a focus dish 100m across is needed to heat up a stationary piece of steel. If you can weaponise a 100m dish, your enemy is going to target it right back.

While the original 2300AD game does get a few things wrong, especially radiating heat and detection ranges, space combat is possible. Remember that within the .01 G threshold (about the asteroid belt in the Sol system) drive efficiency drops to sub-light speeds. This means that it is possible to target other ships with lasers and near light speed weapons such as particle beams and stutterwarp drive missiles. Once a ship moves into the .10 G well than far slower weapons can be used such as railguns, reaction drive missiles and the like.

Deep space combat at above light speed is not possible as the lasers could not catch the target and detection would be near impossible by standard means. There are a few older Challenge Magazine articles that introduce techniques for tracking FTL ships using residual stutterwarp echos but this remains difficult. There are also abundant fan generated discussions concerning combat with stutterwarp ships. Most of these assume that the human warships make use of x-ray lasers which have longer ranges and require smaller focal arrays. Also, given the inherent uncertainty associated with a working stutterwarp drive targeting a specific portion of a warping vessel is extremely difficult. Of course once a vessel is damaged enough to cease warping or enters a .10 G threshold, well than Bob's your uncle, and you can paste the sorry sod.

Deep space combat would be extremely unlikely given how big space is and how small ships are. The likelyhood of two ships coming even remotely close to each other is pretty small. Add to that the speeds and the blinking nature of stutterwarp and the odds of ever seeing another ship on your sensors would be very fractionally above zero.

In the gravity well I think that lasers would have a few distinct problems as Chalkline has clearly described. I remember that Traveller used to also have a defensive system called a sandcaster which threw out clouds of ablative and reflective dust which further reduced the effect of lasers.

I have read about another kind of laser called a shared quantum description beam. Basically the beam is made of entangled photons. Each photon is in a state of quantum entanglement with many other photons which gives it a kind of mass. The beam moves at slightly less than light speed but would hit with greater energy delivered over shorter periods of time. Sounds like just the thing for those pesky moving targets.

I also like the idea of MIRV style missiles. The many warheads can deploy to cover a broad arc of possible travel for the target. Remember they can continually accelerate towards their target so could reach some extreme speeds making it very hard to shoot them down quicky enough.

Wikipedia talks about a missile developed in the 70s, "A second shorter-range missile called Sprint with very high acceleration was added to handle warheads that evaded longer-ranged Spartan. Sprint was a very fast missile (some sources claimed it accelerated to 8,000 mph (13 000 km/h) within 4 seconds of flight—an average acceleration of 100 g) and had a smaller W66 enhanced radiation warhead in the 1-3 kiloton range for in-atmosphere interceptions."

Imagine what the 2300s could develop, plus the benefits of flying in a vacuum...